Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Powerful supercomputer peers into the origin of life

05.10.2010
Supercomputer simulations at the Department of Energy's Oak Ridge National Laboratory are helping scientists unravel how nucleic acids could have contributed to the origins of life.

A research team led by Jeremy Smith, who directs ORNL's Center for Molecular Biophysics and holds a Governor's Chair at University of Tennessee, used molecular dynamics simulation to probe an organic chemical reaction that may have been important in the evolution of ribonucleic acids, or RNA, into early life forms.


New research at Oak Ridge National Laboratory explains how a ribonucleic acid enzyme, or ribozyme (pictured), uses magnesium ions (seen as spheres) to accelerate a significant reaction in organic chemistry.

Certain types of RNA called ribozymes are capable of both storing genetic information and catalyzing chemical reactions - two necessary features in the formation of life. The research team looked at a lab-grown ribozyme that catalyzes the Diels-Alder reaction, which has broad applications in organic chemistry.

"Life means making molecules that reproduce themselves, and it requires molecules and are sufficiently complex to do so," Smith said. "If a ribozyme like the Diels-Alderase is capable of doing organic chemistry to build up complex molecules, then potentially something like that could have been present to create the building blocks of life."

The research team found a theoretical explanation for why the Diels-Alder ribozyme needs magnesium to function. Computational models of the ribozyme's internal motions allowed the researchers to capture and understand the finer details of the fast-paced reaction. The static nature of conventional experimental techniques such as chemical probing and X-ray analysis had not been able to reveal the dynamics of the system.

"Computer simulations can provide insight into biological systems that you can't get any other way," Smith said. "Since these structures are changing so much, the dynamic aspects are difficult to understand, but simulation is a good way of doing it."

Smith explained how their calculations showed that the ribozyme's internal dynamics included an active site, or "mouth," which opens and closes to control the reaction. The concentration of magnesium ions directly impacts the ribozyme's movements.

"When there's no magnesium present, the mouth closes, the substrate can't get in, and the reaction can't take place. We found that magnesium ions bind to a special location on the ribozyme to keep the mouth open," Smith said.

The research was published as "Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme" in the Journal of the American Chemical Society. The research team included Tomasz Berezniak and Mai Zahran, who are Smith's graduate students, and Petra Imhof and Andres Jäschke from the University of Heidelberg.

Smith's research was supported by Laboratory Directed Research and Development program funding. The bulk of the simulations were performed on the Kraken supercomputer at the UT/ORNL National Institute for Computational Sciences, supported by a National Science Foundation Teragrid allocation, and the resulting data were analyzed on the Heidelberg Linux Cluster System at the Interdisciplinary Center for Scientific Computing of the University of Heidelberg.

ORNL is managed by UT-Battelle for the Department of Energy's Office of Science.

Morgan McCorkle | EurekAlert!
Further information:
http://www.ornl.gov

More articles from Information Technology:

nachricht Researchers create new technique for manipulating polarization of terahertz radiation
20.07.2017 | Brown University

nachricht Holograms taken to new dimension
19.07.2017 | University of Utah

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Manipulating Electron Spins Without Loss of Information

Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.

For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...

Im Focus: The proton precisely weighted

What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.

To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...

Im Focus: On the way to a biological alternative

A bacterial enzyme enables reactions that open up alternatives to key industrial chemical processes

The research team of Prof. Dr. Oliver Einsle at the University of Freiburg's Institute of Biochemistry has long been exploring the functioning of nitrogenase....

Im Focus: The 1 trillion tonne iceberg

Larsen C Ice Shelf rift finally breaks through

A one trillion tonne iceberg - one of the biggest ever recorded -- has calved away from the Larsen C Ice Shelf in Antarctica, after a rift in the ice,...

Im Focus: Laser-cooled ions contribute to better understanding of friction

Physics supports biology: Researchers from PTB have developed a model system to investigate friction phenomena with atomic precision

Friction: what you want from car brakes, otherwise rather a nuisance. In any case, it is useful to know as precisely as possible how friction phenomena arise –...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

»We are bringing Additive Manufacturing to SMEs«

19.07.2017 | Event News

The technology with a feel for feelings

12.07.2017 | Event News

Leipzig HTP-Forum discusses "hydrothermal processes" as a key technology for a biobased economy

12.07.2017 | Event News

 
Latest News

Researchers create new technique for manipulating polarization of terahertz radiation

20.07.2017 | Information Technology

High-tech sensing illuminates concrete stress testing

20.07.2017 | Materials Sciences

First direct observation and measurement of ultra-fast moving vortices in superconductors

20.07.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>